transcriptogramStep2-method: Calculates the average of the expression values using a...
In arthurvinx/transcriptogramer: Transcriptional analysis based on transcriptograms

transcriptogramStep2

R Documentation

Calculates the average of the expression values using a sliding window

Description

To each position of the ordering, this method assigns a value equal to the average of the expression values inside a window, region of n (radius * 2 + 1) proteins centered at a protein. The window considers periodic boundary conditions to deal with proteins near the ends of the ordering.

Usage

transcriptogramStep2(object, nCores = 1L)

## S4 method for signature 'Transcriptogram'
transcriptogramStep2(object, nCores = 1L)

Arguments

`object`	An object of class Transcriptogram.
`nCores`	An integer number, referring to the number of processing cores to be used; or a logical value, TRUE indicating that all processing cores should be used, and FALSE indicating the use of just one processing core. The default value of this argument is 1.

Value

This method creates a data.frame to feed the transcriptogramS2 slot of an object of class Transcriptogram. Each row of the data.frame contains: the ENSEMBL Peptide ID used as center of the window, its position on the ordering, and the mean of the expression values of the window.

Author(s)

Diego Morais

References

da Silva, S. R. M., Perrone, G. C., Dinis, J. M., and de Almeida, R. M. C. (2014). Reproducibility enhancement and differential expression of non predefined functional gene sets in human genome. BMC Genomics.

de Almeida, R. M. C., Clendenon, S. G., Richards, W. G., Boedigheimer, M., Damore, M., Rossetti, S., Harris, P. C., Herbert, B. S., Xu, W. M., Wandinger-Ness, A., Ward, H. H., Glazier, J. A. and Bacallao, R. L. (2016). Transcriptome analysis reveals manifold mechanisms of cyst development in ADPKD. Human Genomics, 10(1), 1–24.

Ferrareze, P. A. G., Streit, R. S. A., Santos, P. R. dos, Santos, F. M. dos, de Almeida, R. M. C., Schrank, A., Kmetzsch, L., Vainstein, M. H. and Staats, C. C. (2017). Transcriptional Analysis Allows Genome Reannotation and Reveals that Cryptococcus gattii VGII Undergoes Nutrient Restriction during Infection. Microorganisms.

Morais, D. A. A., Almeida, R. M. C. and Dalmolin, R. J. S. (2019). Transcriptogramer: an R/Bioconductor package for transcriptional analysis based on protein–protein interaction. Bioinformatics.

Rybarczyk-Filho, J. L., Castro, M. A. A., Dalmolin, R. J. S., Moreira, J. C. F., Brunnet, L. G., and de Almeida, R. M. C. (2011). Towards a genome-wide transcriptogram: the Saccharomyces cerevisiae case. Nucleic Acids Research, 39(8), 3005-3016.

Xavier, L. A. da C., Bezerra, J. F., de Rezende, A. A., Oliveira, R. A. de C., Dalmolin, R. J. S., do Amaral, V. S. (2017). Analysis of genome instability biomarkers in children with non-syndromic orofacial clefts. Mutagenesis, 32(2), 313–321.

Examples

transcriptogram <- transcriptogramPreprocess(association, Hs900, 50)
## Not run: 
transcriptogram <- transcriptogramStep1(transcriptogram, GSE9988, GPL570)
transcriptogram <- transcriptogramStep2(transcriptogram)

## End(Not run)

arthurvinx/transcriptogramer documentation built on March 21, 2023, 9:15 a.m.